Yesterday I came across this video (https://www.youtube.com/watch?v=HdTKZKumw8o) from the people of Itkgray (https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/ItkGray). It’s a branch of ItkSnap.
Here you see them using the paintbrush with a ‘Floodfill’ setting for segmenting the white matter of the brain.
- Set the active drawing label to ‘white’ with the correct hemisphere.
- Use the Paintbrush tool to fill in most of the white matter and the ventricles.
The axial view works well for this; using Floodfill with the 3D brush on at a tolerance of ~5 and/or the square and round brush. - It may help to start dorsally and work down, cleaning up the subcortical areas as you progress.
I was wondering if this option is also available in Slicer? I haven’t found it (yet) and from what I noticed, it now only works on the entire 3D-image and you can’t contain it to only a brushsize or other volume.
Or is there maybe a workaround for this? My idea would be to do a coarse, completely filled segmentation with for instance the ‘Fill between slices’ option and then use the ‘Flood filling’, constrained to the coarse segmentation.
Any other suggestions?